Variant report

Variant	rs6888883
Chromosome Location	chr5:179444395-179444396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179443617..179446152-chr5:179448678..179450322,2	MCF-7	breast:
2	chr5:179442610..179444709-chr5:179448350..179450019,2	K562	blood:
3	chr5:179439048..179442234-chr5:179444024..179447573,4	K562	blood:
4	chr5:179443209..179445457-chr5:179448507..179450019,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036834	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10045755	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10051632	0.86[EUR][1000 genomes]
rs10061480	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10068529	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068594	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10078977	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479455	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10903246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1102190	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153541	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12653944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173562	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs185076	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs193718	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs248257	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248258	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248316	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs248319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs27014	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27016	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27017	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs27019	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35928331	0.86[ASN][1000 genomes]
rs394588	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4130025	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs418384	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4340879	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4466125	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs449511	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55734821	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62405020	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405021	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871596	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7706570	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs857181	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs857182	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs857183	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs857189	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9329096	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:179426400-179447200	Weak transcription	A549	lung
5	chr5:179427000-179447400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:179427400-179447200	Weak transcription	Hela-S3	cervix
7	chr5:179428600-179447200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:179429000-179447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:179429400-179447200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179429400-179452800	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:179429600-179446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:179429600-179447000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:179429800-179445600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:179429800-179446800	Weak transcription	Gastric	stomach
16	chr5:179429800-179447200	Weak transcription	Placenta	Placenta
17	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:179430000-179453000	Weak transcription	NH-A	brain
22	chr5:179430600-179462400	Weak transcription	HepG2	liver
23	chr5:179434800-179447000	Weak transcription	Fetal Kidney	kidney
24	chr5:179434800-179448200	Weak transcription	Fetal Heart	heart
25	chr5:179435000-179446400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:179435000-179447200	Weak transcription	Spleen	Spleen
27	chr5:179435200-179448800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:179435400-179447000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:179435400-179447200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179435400-179453400	Weak transcription	Right Atrium	heart
31	chr5:179435800-179446800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:179435800-179454600	Weak transcription	K562	blood
33	chr5:179436200-179449200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:179436200-179450600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:179436600-179445200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:179436800-179447400	Weak transcription	Fetal Lung	lung
37	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:179439200-179452600	Weak transcription	HUVEC	blood vessel
40	chr5:179439400-179447000	Weak transcription	HSMMtube	muscle
41	chr5:179439400-179447200	Weak transcription	Right Ventricle	heart
42	chr5:179439600-179445600	Weak transcription	Lung	lung
43	chr5:179439600-179446800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:179439600-179447000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:179439600-179447000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:179439600-179447000	Weak transcription	Pancreas	Pancrea
47	chr5:179439600-179453400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:179439800-179446600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:179439800-179446800	Weak transcription	Brain Germinal Matrix	brain
50	chr5:179439800-179448000	Weak transcription	Primary B cells from cord blood	blood

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